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Job settings #1473
Job #1473 review -
http://beta.mole.upol.cz/online/1473/
Generated on 2024-04-26 12:08:36 by service v.
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Settings
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Structure:
1tqn
(
structure summary on pdb.org
)
Unit:
1
Chain:
1
Automatic starting points
Identify tunnels starting from multiple cavities. This can provide a good initial insight into the tunnel structure of the protein.
Starting point
:
Example: GLU 308, THR 309
The starting point is defined as a center of mass of selected residues. You can choose residues using by the sequence inspector below the Jmol window. In case you analyze an enzyme structure, MOLEOnline offers an active site residues (from the Catalytic Site Atlas, if available) as the starting point.
Active sites from
CSA
:
A GLU 308, A THR 309
A THR 309, A PHE 435, A CYS 442
Automatic end points
End point
:
Ignore all HETATM
Ignoring coordinates with HETATM records for non-polymer or other “non-standard” chemical coordinates, such as atoms presented in HET groups (ligands, prosthetic groups) in PDB format. Reminder: water molecules (WAT, HOH, SOL) are ignored everytime in MOLEonline 2.0!
Advanced Settings
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Ignored residues
:
Example: A GLU 308, B THR 309.
List of residues to be ignored prior computation of channel.
Starting point [X,Y,Z]:
Specify starting point as an X, Y, Z coordinates (as decimal numbers in Å).
Ending point [X,Y,Z]:
Specify ending point as an X, Y, Z coordinates (as decimal numbers in Å).
Probe Radius
:
Radius used for construction of molecular surface.
Interior Threshold
:
Lower bound of the tunnel radius.
Surface Cover Radius
:
Determines the density of tunnel exits on the molecular surface.
Origin Radius
:
Better starting points are localized within the defined radius from the original starting point.
Bottleneck Radius
:
Tunnels with bottleneck bellow this radius will be removed.
Max Tunnel Similarity Radius
:
Used to remove tunnels based on their percentage similarity.
reset
to default values